Did you play them already? Don't want to spoil anything for you.
In short, Avernum is a lot bigger, plays underground, and is a lot more open exploration.
Avadon is more streamlined/linear, and felt smaller to me than Avernum.
Anyways, I really liked them all, great storytelling which you don't see often anymore.
I have avernum 6. And love it. Was wondering how the other spiderweb games compare on iPad.
They are pretty much near identical on iPad if you've played the PC versions. As the other poster stated above, one series in more linear and the other more open ended, one allows for creating custom characters, the other does not, but both are excellent games. I own all of them for the iPad (and pretty near the complete collection of Spederweb games on PC) and if you are looking for an in depth, old school CRPG you will love these games!
They all were a great experience, and played extremely well on in my iPad2 and later Air.
The only gripe I have is that the UI - especially Avernum's - is too small. But nowhere near as bad as the Baldur's Gates games.
I play with a stylus - "thanks" to my RSI, wouldn't use one if I hadn't developed that - and for the Spiderweb (and many other) games it is much better than without.